Vector-borne diseases such as malaria and dengue hemorrhagic fever remain large public health burdens, and novel interventions are still needed. The emerging field of genetics-based control has seen a number of recent laboratory successes with the generation of pathogen- resistant mosquito strains as well as female-killing strains. The development of genetically modified mosquitoes still largely relies upon classical transposable element transformation, although several recent reports have made use of the site-specific integrase C31. While site- specificity allows the investigator to examine multiple transgenes in the same genetic environment, an unfortunate consequence of the attP-attB C31 system is that as a result of recombination the entire bacterial plasmid becomes integrated into the mosquito genome. This is undesirable, as many of the currently developed transgenic mosquito strains are intended as specific genetic interventions to control a targeted vector-borne pathogen where such antibiotic resistance genes could be transferred to native bacterial species. We hypothesize that recombinase-mediated cassette exchange (RMCE) can be an efficient means of delivering transgenes into important disease vector species in a site-specific manner, without the negative consequences of co-integrating bacterial sequences. As such, we propose to (1) test a panel of heterospecific lox sites for their ability to resist intramolecular recombination i cis and promote RMCE in the embryos of the dengue vector Aedes aegypti and the malaria vector Anopheles gambiae; (2) generate transgenic docking strains based on the best candidate heterospecific lox sites and determine the rate of RMCE for each using the phage P1 cre recombinase. Such an alternative system which preserves the ability to perform site-specific recombination, but avoids the integration of bacterial sequences and remains as easy to use as TE-based helper plasmids would likely be much more widely adopted, and would help to drive the field of novel genetics- based control strategies for vector-borne diseases.